Computational comparative genomics of the scabies mite

Computational comparative genomics of the scabies mite

Project details

Scabies is an infectious skin infestation caused by the parasitic scabies mite. It is a major health problem in Indigenous communities in Northern Australia, and is thought to underlie bacterial skin infections which lead to rheumatic fever and subsequent rheumatic heart disease and chronic kidney disease. Indigenous Australians have amongst the highest rates of these diseases in the world.

To accelerate research into scabies, we have previously sequenced and assembled the scabies mite genome using Illumina short reads (Mofiz et al, GigaScience 2016, 5:23) and used this to investigate the genetic diversity of individual patient infestations (Mofiz et al, PLoS Negl Trop Dis. 2016, 10(2):e0004384). We have also generate other transcriptomic and proteomic resources from the scabies mite. The Institute recently purchased a PacBio Seque, which produces long reads, and we plan to use this to generate a high quality assembly.

The main focus of this project will be to generate new biological insights using computational comparative genomics. The research student will develop skills in biological sequence analysis and genome informatics, and contribute important understanding to this neglected disease.

About our research group

The Papenfuss lab uses mathematics, statistics and computation to understand the evolution  of cancer, as well as other diseases. This frequently entails the development of novel bioinformatics, computational and mathematical methods to make sense of complex biological data, for example tools for discovering genomic rearrangements. Lab members comprise mathematicians, statisticians, computer scientists, physicists, as well as biologists.

We have been involved in multiple genome and transcriptome projects including playing leading roles in the tammar wallaby genome project. Our work is enabled by the Institute's new high performance computing resources.

This project is part of an initiative in Indigenous health research at the Institute. It involves collaboration with Dr Katja Fischer at QIMR Berghofer and Dr Deb Holt at the Menzies School of Health Research in Darwin.

Researchers:

Associate Professor Tony Papenfuss

Tony Papenfuss
Associate Professor
Tony
Papenfuss
Head, Computational Biology; Laboratory Head

Project Type: